[Chimera-users] thermal ellipsoids

[Dipl.-Ing. Thomas Mitterfellner]

Hello!

Thanks for the information concerninge the scaling factors.

> Given the way the underlying ellipsoid depiction is generated, it won't
> be easy. Nonetheless, I do think it should happen but it will take
> awhile. One thing that would be easy for me to do would be to actually
> show the ellipsoid axes (as lines). Would this help any if I put it in
> there?

If I understand it correctly, the ellipsoid axes you mentioned would be 
invisible if I the ellipsoids are rendered 100% opaque, right? So it for 
me, personally, it won't help, but probably for others.
I was just thinking about the three ellipses that make up each 
ellipsoid to be shown on the surface.

Concerning the CIF file, I was talking about a small molecule CIF. 
Unfortunately, I don't know about the mmCIF format.

The information in my CIF is encoded like this:
<snip>
  _atom_site_label
  _atom_site_type_symbol
  _atom_site_fract_x
  _atom_site_fract_y
  _atom_site_fract_z
  _atom_site_U_iso_or_equiv
  _atom_site_adp_type
  _atom_site_occupancy
  _atom_site_symmetry_multiplicity
  _atom_site_calc_flag
  _atom_site_refinement_flags
  _atom_site_disorder_assembly
  _atom_site_disorder_group
Si1 Si 0.27946(5) 0.08326(9) 0.39479(4) 0.0163(3) Uani 1 1 d . . .
H1 H 0.2704 0.1083 0.4766 0.034 Uiso 1 1 calc R . .
</snip>

This is an example for one anisotropic atom and an isotropic one. Later 
on in the file, from how I understand it, there seems to be the actual 
ellipsoid information:

<snip>
  _atom_site_aniso_label
  _atom_site_aniso_U_11
  _atom_site_aniso_U_22
  _atom_site_aniso_U_33
  _atom_site_aniso_U_23
  _atom_site_aniso_U_13
  _atom_site_aniso_U_12
Si1 0.0181(5) 0.0176(5) 0.0126(5) -0.0010(3) 0.0038(4) -0.0003(4)
</snip>

Kind regards,

Thomas